Molecular dynamics study of 2rotaxanes: influence of solvation and cation on co-conformation

The conformational preference of a [2]rotaxane system has been examined by molecular dynamics simulations. The rotaxane wheel consists of two bridged binding components: a cis-dibenzo-18-crown-6 ether and a 1,3-phenyldicarboxamide, and the penetrating axle consists of a central isophthaloyl unit with phenyltrityl capping groups. The influence of solvation on the co-conformation of the [2]rotaxane was evaluated by comparing the conformational flexibility in two solvents: chloroform and dimethyl sulfoxide. Attention was also paid to the effect of cation binding on the dynamical properties of the [2]rotaxane. The conformational stability of the [2]rotaxane was calculated using a MM/PB-SA strategy, and the occurrence of specific motions was examined by essential dynamics analysis. The changes in the co-conformational properties in the two solvents and upon cation binding are discussed in light of the available NMR data. The results indicate that in chloroform solution the [2]rotaxane system exists as a mixture of co-conformational states including some that have hydrogen bonds between axle C=O and wheel NH groups. Analysis of the simulations allow us to hypothesize that the [2]rotaxane's circumrotation motion can occur as the result of a dynamic process that combines a preliminary axle sliding step that breaks these hydrogen bonds and a conformational change in the ester group more distant from the wheel. In contrast, no hydrogen-bonded co-conformation was found in dimethyl sulfoxide, which appears to be due to the preferential formation of hydrogen bonds between the wheel NH groups with solvent molecules. Moreover, the axle experiences notable changes in anisotropic shielding, which would explain why the NMR signals are broadened in this solvent. Insertion of a sodium cation into the crown ether reduces co-conformational flexibility due to an interaction of the axle with the cation. Overall, the results reveal how both solvent and ionic atmosphere can influence the co-conformational preferences of rotaxanes.     

A self-threaded "molecular 8"

A new type of [1]rotaxanes containing two aliphatic bridges between axle and wheel is obtained in 39% yield in a one-step synthesis starting from a [2]rotaxane which contained one sulfonamide group each in both the wheel and the axle. Temperature controlled chemoselective substitution reactions first at these sulfonamide nitrogens and then subsequently at the various other carboxamide nitrogens in the wheel and axle give rise to the formation of an isomeric mixture of three double-bridged [1]rotaxanes which could be separated by HPLC. Structure determination of the main product 3a was possible by NMR experiments supported by molecular modeling calculations. Using different reaction conditions, a double-substituted but not yet bridged [2]rotaxane 4 could be isolated as an intermediate giving further evidence for the assigned structure of 3a and the way of its formation. The shape of this double-bridged [1]rotaxane 3a reminds of a self-intertwining chiral "molecular 8", in which any possible racemization due to deslipping is hindered by the two stoppers originating from the former rotaxane axle. Hence, to the best of our knowledge this is the first example of a molecule in which both concepts, cycloenantiomerism and helical chirality, are realised in one structure. Enantiomer separation of the main product was possible by further HPLC using chiral stationary phases. The Cotton effects of the circular dichrograms are different to those of the already synthesized [1]rotaxanes bearing just one aliphatic bridge between axle and wheel.     

Quantitative conformational study of redox-active [2]rotaxanes, part 1: Methodology and application to a model [2]rotaxane

This paper reports a novel methodology for the conformational analysis of [2]rotaxanes. It combines NMR spectroscopic (COSY, NOESY and the recently reported paramagnetic line-broadening and suppression technique) and electrochemical techniques to enable a quantitative analysis of the co-conformations of interlocked molecules and the conformations of their components. This methodology was used to study a model [2]rotaxane in solution. This [2]rotaxane consists of an axle that incorporates an electron-poor, doubly positively charged viologen that threads an electron-rich crown ether. It has been shown that the axle of the [2]rotaxane in its dicationic state adopts a folded conformation in solution and the crown ether is localised at the viologen moiety. Following a one-electron reduction of viologen, the paramagnetic radical cation of the [2]rotaxane retains its folded conformation in solution. The data also demonstrate that in the radical cation the crown ether remains localised at the viologen, despite its reduced affinity for the singly reduced viologen. The combined quantitative NMR spectroscopic and electrochemical characterisation of the electromechanical function of the model [2]rotaxane in solution provides an important reference point for the study of switching in structurally related bistable [2]rotaxanes, which is the subject of the second part of this work.     

The Effect of Incorporating Fréchet Dendrons into Rotaxanes and Molecular Shuttles Containing the 1,2‐Bis(pyridinium)ethane⊂[24]Crown‐8 Templating Motif

Fréchet‐type dendrons (G0–G3) were added as both axle stoppering units and cyclic wheel appendages in a series of [2]rotaxanes, [3]rotaxanes, and molecular shuttles that employ 1,2‐bis(pyridinium)ethane axles and 24‐membered crown ethers wheels. The addition of dendrimer wedges as stoppering units dramatically increased the solubility of simple [2]rotaxanes in nonpolar solvents. The X‐ray structure of a G1‐stoppered [2]rotaxane shows how the dendritic units affect the structure of the interlocked components. Increased solubility allows observation of how the interaction of dendritic units on separate components in interlocked molecules influences switching properties and molecular size. In a series of [2]rotaxane molecular shuttles incorporating two recognition sites, it was demonstrated that an increase in generation on either the stoppering unit or cyclic wheel could influence both the rate of shuttling and the site preference of the wheel on the axle.     

Rational Design for Rotaxane Synthesis through Intramolecular Slippage: Control of Activation Energy by Rigid Axle Length

We describe a new concept for rotaxane synthesis through intramolecular slippage using π‐conjugated molecules as rigid axles linked with organic soluble and flexible permethylated α‐cyclodextrins (PM α‐CDs) as macrocycles. Through hydrophilic–hydrophobic interactions and flipping of PM α‐CDs, successful quantitative conversion into rotaxanes was achieved without covalent bond formation. The rotaxanes had high activation barrier for their de‐threading, so that they were kinetically isolated and derivatized even under conditions unfavorable for maintaining the rotaxane structures. ¹H NMR spectroscopy experiments clearly revealed that the restricted motion of the linked macrocycle with the rigid axle made it possible to control the kinetic stability by adjusting the length of the rigid axle in the precursor structure rather than the steric bulkiness of the stopper unit.     

Accordion‐Like Motion in Electrochemically Switchable Crown Ether/Ammonium Oligorotaxanes

Reversible oxidation reactions in electrochemically switchable oligorotaxanes with tetrathiafulvalene (TTF) decorated 24‐crown‐8 ether wheels generate intramolecular mixed‐valence and radical‐cation interactions between the wheels. This induces shuttling of the wheels and a contraction of inter‐wheel distances. Further oxidation generates repulsive forces between the TTFs and maximizes the inter‐wheel distances instead. These interactions and co‐conformational changes were not observed for structurally similar controls in which acetyl groups along the axle prevent translational motion of the wheels. This operation mode of oligorotaxanes, which is reminiscent of an accordion‐like motion, is promising for functional materials and nanodevices such as piston‐type rotaxane motors.     

1]rotaxanes and pretzelanes: synthesis, chirality, and absolute configuration [In Process Citation

The synthesis of aliphatically bridged [1](n)rotaxanes and (n)pretzelanes in preparative yields and the dependency of their chiroptical properties on the length (n) of their bridge are reported. A cycloenantiomeric bis(sulphonamide)[2]rotaxane with a sulphonamide group in its axle and its wheel was intramolecularly dialkylated by homologous bifunctional oligomethylene reagents to form chiral [1](n)rotaxanes bearing bridges of different lengths (n) between the axle and the wheel. Intramolecular dialkylation by 1,omega-dibromoalkanes of a topologically chiral bis(sulphonamide)[2]catenane with a sulphonamide group in both of the macrolactam rings leads to pretzel shaped molecules ((n)pretzelanes) with homologous bridges between the two macrocycles. Their yields decrease with decreasing length of the bridge. The shortest bridge isolated so far in reasonable amounts consists of six methylene groups ((6)pretzelane). Remarkably, a covalent connection of axle and wheel in a [2]rotaxane was successful even with much shorter bridges-down to only three methylene groups ([1](3)rotaxane). The structural changes of the [1](n)rotaxanes with decreasing bridge length is expressed by an increasing high-field shift in the 1H NMR spectra. Enantiomeric resolution of the racemates of both series was achieved in seven cases for the [1](n)rotaxanes and two for the (n)pretzelanes by use of chiral HPLC columns. The circular dichrograms of both compound families show a strong dependency on the length of the bridge. However, the shortest bridges displayed some additional unexpected deviations. A new specification of the absolute configuration of supramolecules, such as [n]catenanes, [n]rotaxanes and (n)pretzelanes is introduced together with some nomenclature additions.     

Synthesis and characterization of a metallocycle-based molecular shuttle

Kinetically stable metallocycle-based molecular shuttles of [2]rotaxanes 4a and 4b, along with [3]rotaxanes 5a and 5b, have been prepared using the rhenium(I)-bridged metallocycle 2 and the dumbbell components containing two stations, 3a and 3b. The rotaxanes were self-assembled by hydrogen bonding interactions upon heating a Cl(2)CHCHCl(2) solution containing their components at 70 degrees C. Each rotaxane was isolated in pure form by silica gel chromatography under ordinary laboratory conditions and fully characterized by elemental analysis and various spectroscopic methods. The (1)H NMR signals for the amide NH and the methylene -(CH(2))(4)- of the station were considerably changed when occupied by the metallocycle. In [2]rotaxane 4b, which has a larger naphthyl spacer, the occupied and unoccupied stations gave widely separated signals in the (1)H NMR spectroscopy at room temperature, but averaged signals of two stations were observed in [2]rotaxane 4a, which has a smaller phenyl spacer. This is attributed to the shuttling of the metallocycle between two stations. The coalescence temperature experiment gave a shuttling rate of approximately 670 s(-)(1) at 19 degrees C in CDCl(3), corresponding to an activation free energy (DeltaG()) of 13.3 kcal/mol. With respect to the relative position of the chloride in the rhenium(I) center, two diastereomers are possible in the [2]rotaxane and three diastereomers are possible in the [3]rotaxane. In fact, the rotaxanes exist as diastereomeric mixtures in nearly equal amounts of all possible diastereomers on the basis of the amide NH signals of the station in the (1)H NMR spectroscopy.     

Unveiling the Hidden Movements in the Shuttling of Rotaxanes

Movements in molecular machines are usually diverse and coupled, but some of them are often implicit and hard to be observed in experiments. In the present work, the two-or three-dimensional free-energy landscapes characterizing the coupled shuttling and other movements of a series of pH-triggered rotaxanes composed of a crown ether and an H-shaped axle with distinct number of phenyl rings(n=1-3) have been explored. The results show that although the calculated free-energy barriers against shuttling in the rotaxanes(n=2 and 3) change slightly, the movements coupled with the shuttling vary significantly with the axle length. At high pH, the shuttling in the rotaxane of n=2 is coupled with the isomerization of the wheel, while the shuttling in the one of n=3 is accompanied by both the isomerization and the rotation of the macrocycle. In addition, the crown ether underwent greater conformational change during shuttling at low pH compared to that at high pH. These results indicate that disentangling the coupled movements is important to reveal the underlying molecular mechanism of the shuttling.     

Chiral [1]Rotaxanes: X‐Ray Structures and Chiroptical Properties

New chiral [1]rotaxanes with aromatic bridges were prepared in yields up to 72% starting from a [2]rotaxane with sulfonamide groups in wheel and axle. The X‐ray structures of the parent [2]rotaxane 1 and of the three [1]rotaxanes 3e , g , h were solved which show networks of H‐bonds between wheel and axle. The separation of the racemic mixtures of four of the [1]rotaxanes, i.e., of 3a , b , d , e , was possible with HPLC on Chiralcel OD. The aromatic chromophores in the bridges lead to a considerable enhancement of the intensities of the molar CD as compared to the analogues with aliphatic bridges. In one case ( 3d ), the Cotton effects are as strong as those usually found in helicenes.     

2]Rotaxanes containing pyridinium-phosphonium axles and 24-crown-8 ether wheels

A triethylphosphonium group attached to a pyridinium ethane moiety can be used as an axle for the self-assembly of [2]pseudorotaxanes and [2]rotaxanes. Although [2]pseudorotaxane formation is limited due to the bulk of the PR4+ group, [2]rotaxanes can be formed utilising 24-crown-8 ether, benzo-24-crown-8 ether and naphtho-24-crown-8 ether. The synthesis of these [2]rotaxanes and the X-ray structure of the [2]rotaxane containing a 24-crown-8 ether wheel are described. When the crown ether contains an aromatic group two possible conformational isomers exist; these are identified at low temperature by 1H and 31P NMR spectroscopy.     

Cationic and Neutral Rotaxanes Having Different Functional Groups in the Axle Molecule and Their Coordination to PtII

Dibenzo[24]crown‐8 (DB24C8) forms rotaxanes with a linear molecule having a dialkylammonium group and a triazole group as well as with the acetylation product of a cationic axle molecule. The former cationic rotaxane is stabilized by multiple intermolecular hydrogen bonds between the NH₂⁺ and oxyethylene groups. The neutral rotaxane contains the macrocycle in the vicinity of the terminal aryl group. The co‐conformation of both the cationic and neutral rotaxanes can be fixed by coordination of the triazole group of the axle molecule to PtCl₂(dmso)₂. A ¹H NMR spectroscopic study on the thermodynamics of the Pt coordination revealed a larger association constant for the rotaxanes than for the corresponding axle molecules and a larger value for the neutral rotaxane than for the cationic rotaxane.     

Anion-induced shuttling of a naphthalimide triazolium rotaxane

The anion-templated synthesis of a rotaxane structure, incorporating the new naphthalimide triazolium motif, is described and the interlocked host shown to exhibit selective, uni-directional, anion-induced shuttling. Initial pseudorotaxane investigations demonstrate the ability of a naphthalimide triazolium threading component to form interpenetrated assemblies with counter-anion-dependent co-conformations. (1)H NMR studies reveal that the shuttling behaviour of the analogous rotaxane host system is controlled by selective anion binding and by the nature of the solvent conditions. Complete macrocycle translocation only occurs upon the recognition of the smaller halide anions (chloride and bromide). The rotaxane solid-state crystal structure in the presence of chloride is in agreement with the solution-phase co-conformation. The sensitivity of the axle naphthalimide absorbance band to the position of the macrocycle component within the interlocked structure enabled the molecular motion to be observed by UV/Vis spectroscopy, and the chloride-induced shuttling of the rotaxane was reversed upon silver hexafluorophosphate addition.     

Anion recognition and cation-induced molecular motion in a heteroditopic [2]rotaxane

A heteroditopic [2]rotaxane consisting of a calix[4]diquinone–isophthalamide macrocycle and 3,5‐bis‐amide pyridinium axle components with the capability of switching between two positional isomers in response to barium cation recognition is synthesised. The anion binding properties of the rotaxane’s interlocked cavity together with Na⁺, K⁺, NH₄⁺ and Ba²⁺ cation recognition capabilities are elucidated by ¹H NMR and UV‐visible spectroscopic titration experiments. Upon binding of Ba²⁺, molecular displacement of the axle’s positively charged pyridinium group from the rotaxane’s macrocyclic cavity occurs, whereas the monovalent cations Na⁺, K⁺ and NH₄⁺ are bound without causing significant co‐conformational change. The barium cation induced shuttling motion can be reversed on addition of tetrabutylammonium sulfate.     

Effects of Axle‐Core,Macrocycle, and Side‐Station Structures on the Threading and Hydrolysis Processes of Imine‐Bridged Rotaxanes

Imine‐bridged rotaxanes are a new type of rotaxane in which the axle and macrocyclic ring are connected by imine bonds. We have previously reported that in imine‐bridged rotaxane 5 , the shuttling motion of the macrocycle could be controlled by changing the temperature. In this study, we investigated how the axle and macrocycle structures affect the construction of the imine‐bridged rotaxane as well as the dynamic equilibrium between imine‐bridged rotaxane 5 and [2]rotaxane 7 by using various combinations of axles ( 1 A , B ), macrocycles ( 2 a – e ), and side‐stations (XYL and TEG). In the threading process, the flexibility of the macrocycle and the substituent groups at the para position of the aniline moieties affect the preparation of the threaded imines. The size of the imine‐bridging station and the macrocyclic tether affects the hydrolysis of the imine bonds under acidic conditions.     

Size Complementarity of Macrocyclic Cavities and Stoppers in Amide-Rotaxanes

New [2]rotaxanes were prepared by the threading and the slipping procedure, the latter having the advantage of not needing templating interactions. As a consequence, the first [2]rotaxane consisting of a tetraamide macrocycle and a pure hydrocarbon thread was synthesized (see 12a in Scheme 2). Sterically matching wheels and axles being the basic requirement of a successful slipping approach to rotaxanes, mono- and bishomologous wheels 5b , c with larger diameters than the parent 5a were synthesized and mechanically connected to amide axles 10a – c which were stoppered with blocking groups of different spatial demand (Scheme 1). The deslipping kinetics of the resulting rotaxanes 8a – c and 9a , b were measured and compared; it emerges that even slight increases in the wheel size require larger stoppers to stabilize the mechanical bond. Moreover, when the deslipping rate of 8a (amide wheel and amide axle) was determined in either DMF or THF, a strong dependence on the solvent polarity, which is caused by a differing extent of intramolecular H-bonds between the wheel and the axle, was observed. As expected, no such dependence was detected for rotaxane 12a (amide wheel and hydrocarbon axle) whose components cannot interact via H-bonds. The comparison of the sterically matching pairs of macrocycles and blocking groups, found by a systematic fitting based on the results of slipping and deslipping experiments, with other rotaxane types bearing similar stoppers allows conclusions concerning the relative cavity size of wheels of various structure.     

Asymmetric benzoin condensation catalyzed by chiral rotaxanes tethering a thiazolium salt moiety via the cooperation of the component: can rotaxane be an effective reaction field?

Although some reactions on rotaxanes have been reported, the characteristic features of the rotaxanes providing unique reaction fields have hardly been studied, especially as catalyst. In our continuous studies on interlocked molecules such as rotaxanes and catenanes, we have noticed the importance of such interlocked structures with high freedom in functionalized materials such as molecular catalyst. For catalytic asymmetric benzoin condensations, two optically active rotaxanes possessing thiazolium salt moieties were prepared using the binaphthyl group as the chiral auxiliary. The benzoin condensations of aromatic aldehydes catalyzed by the chiral rotaxanes as catalysts gave optically active benzoins with ca. 30% ee in moderate to high chemical yields depending upon the structure of rotaxane and the reaction conditions employed. From the results, two intrarotaxane chirality transfers are confirmed: (i) through-space chirality transfer from wheel to axle and (ii) through-bond chirality transfer controlled with an achiral wheel. Because these asymmetric reaction fields are specific to the rotaxane structure, the importance and possibility of the "rotaxane field" as a particular reaction field is demonstrated in this work.     

Sequential O- and N-acylation protocol for high-yield preparation and modification of rotaxanes: synthesis, functionalization, structure, and intercomponent interaction of rotaxanes

A pseudorotaxane consisting of a 24-membered crown ether and secondary ammonium salt with the hydroxy group at the terminus was quantitatively acylated by bulky acid anhydride in the presence of tributylphosphane as catalyst to afford the corresponding rotaxane in high yield. Large-scale synthesis without chromatographic separation was easily achieved. The ammonium group in the resulting rotaxane was quantitatively acylated with excess electrophile in the presence of excess trialkylamine. Various N-functionalized rotaxanes were prepared by this sequential double-acylation protocol. 1H NMR spectra and X-ray crystallographic analyses of the rotaxanes showed that the crown ether component was captured on the ammonium group in ammonium-type rotaxane by strong hydrogen-bonding intercomponent interaction. The conformation around the ammonium group was fixed by the hydrogen-bonding interaction. Meanwhile, the conformation of the amide-type rotaxane was determined by the weak CH/pi interaction between the methylene group in crown ether and the benzene ring of the axle component. The N-acylation of ammonium-type rotaxane is useful for the preparation of both functionalized rotaxanes and weak intercomponent interaction-based rotaxanes.     

Anion‐Induced Shuttling of a Naphthalimide Triazolium Rotaxane

The anion‐templated synthesis of a rotaxane structure, incorporating the new naphthalimide triazolium motif, is described and the interlocked host shown to exhibit selective, uni‐directional, anion‐induced shuttling. Initial pseudorotaxane investigations demonstrate the ability of a naphthalimide triazolium threading component to form interpenetrated assemblies with counter‐anion‐dependent co‐conformations. ¹H NMR studies reveal that the shuttling behaviour of the analogous rotaxane host system is controlled by selective anion binding and by the nature of the solvent conditions. Complete macrocycle translocation only occurs upon the recognition of the smaller halide anions (chloride and bromide). The rotaxane solid‐state crystal structure in the presence of chloride is in agreement with the solution‐phase co‐conformation. The sensitivity of the axle naphthalimide absorbance band to the position of the macrocycle component within the interlocked structure enabled the molecular motion to be observed by UV/Vis spectroscopy, and the chloride‐induced shuttling of the rotaxane was reversed upon silver hexafluorophosphate addition.     

Halotriazolium Axle Functionalised [2]Rotaxanes for Anion Recognition: Investigating the Effects of Halogen‐Bond Donor and Preorganisation

The anion‐templated synthesis of three novel halogen‐bonding 5‐halo‐1,2,3‐triazolium axle containing [2]rotaxanes is described, and the effects of altering the nature of the halogen‐bond donor atom together with the degree of inter‐component preorganisation on the anion‐recognition properties of the interlocked host investigated. The ability of the bromotriazolium motif to direct the halide‐anion‐templated assembly of interpenetrated [2]pseudorotaxanes was studied initially; bromide was found to be the most effective template. As a consequence, bromide anion templation was used to synthesise the first bromotriazolium axle containing [2]rotaxane, the anion‐binding properties of which, determined by ¹H NMR spectroscopic titration experiments, revealed enhanced bromide and iodide recognition relative to a hydrogen‐bonding protic triazolium rotaxane analogue. Two halogen‐bonding [2]rotaxanes with bromo‐ and iodotriazolium motifs integrated into shortened axles designed to increase inter‐component preorganisation were also synthesised. Anion ¹H NMR spectroscopic titration experiments demonstrated that these rotaxanes were able to bind halide anions even more strongly, with the iodotriazolium axle integrated rotaxane capable of recognising halides in aqueous solvent media. Importantly, these observations suggest that a halogen‐bonding interlocked host binding domain, in combination with increased inter‐component preorganisation, are requisite design features for a potent anion receptor.